Abstract
MotivationBiomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility.ResultsThe Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications.ConclusionThe SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user’s needs.AvailabilityThe Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.
Highlights
IntroductionWe report on the Software Ontology (SWO) [1,2], an ontology for describing the software used within computational biology, which includes bioinformatics resources and any software tools used in the preparation and maintenance of data
The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on
The Software Ontology (SWO) is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered
Summary
We report on the Software Ontology (SWO) [1,2], an ontology for describing the software used within computational biology, which includes bioinformatics resources and any software tools used in the preparation and maintenance of data. Development of the SWO is motivated by the growing interest in the recording and reproducibility of biomedical investigations [3,4]. Reproducibility is as important for computational investigations of data as it need to be known - and even the hardware upon which it was run, as all of these can have an influence on the results obtained. There has been a move to automatically describe the provenance of computations (including the actual run of a workflow), and ontologies have been provided to support this recording [12]. An ontology such as the SWO provides the vocabulary and identifiers for the software aspects of such automatically recorded provenance
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